Starting phenix.real_space_refine on Wed Sep 17 03:31:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u4u_63855/09_2025/9u4u_63855.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u4u_63855/09_2025/9u4u_63855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9u4u_63855/09_2025/9u4u_63855.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u4u_63855/09_2025/9u4u_63855.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9u4u_63855/09_2025/9u4u_63855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u4u_63855/09_2025/9u4u_63855.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1881 2.51 5 N 609 2.21 5 O 714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3204 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'TRANS': 149} Chain breaks: 5 Restraints were copied for chains: B, C Time building chain proxies: 0.85, per 1000 atoms: 0.27 Number of scatterers: 3204 At special positions: 0 Unit cell: (64.308, 55.92, 58.716, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 714 8.00 N 609 7.00 C 1881 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.27 Conformation dependent library (CDL) restraints added in 224.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 804 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 64 removed outlier: 6.257A pdb=" N ASN A 62 " --> pdb=" O ASN A 128 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ASN B 62 " --> pdb=" O ASN B 128 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASN C 62 " --> pdb=" O ASN C 128 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 82 removed outlier: 3.662A pdb=" N SER A 73 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N SER A 138 " --> pdb=" O SER A 212 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 210 through 213 current: chain 'B' and resid 72 through 83 removed outlier: 3.663A pdb=" N SER B 73 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N SER B 138 " --> pdb=" O SER B 212 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 210 through 213 current: chain 'C' and resid 72 through 83 removed outlier: 3.662A pdb=" N SER C 73 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N SER C 138 " --> pdb=" O SER C 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 92 removed outlier: 6.296A pdb=" N ASN A 157 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N THR A 230 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASN B 157 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR B 230 " --> pdb=" O ALA C 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 178 removed outlier: 6.317A pdb=" N GLN A 176 " --> pdb=" O VAL B 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.307A pdb=" N GLN B 176 " --> pdb=" O VAL C 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 62 hydrogen bonds defined for protein. 186 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.58 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 645 1.29 - 1.35: 576 1.35 - 1.42: 120 1.42 - 1.48: 480 1.48 - 1.55: 1380 Bond restraints: 3201 Sorted by residual: bond pdb=" CA GLN C 113 " pdb=" C GLN C 113 " ideal model delta sigma weight residual 1.529 1.517 0.012 1.04e-02 9.25e+03 1.23e+00 bond pdb=" CA GLN B 113 " pdb=" C GLN B 113 " ideal model delta sigma weight residual 1.529 1.518 0.011 1.04e-02 9.25e+03 1.18e+00 bond pdb=" CA GLN A 113 " pdb=" C GLN A 113 " ideal model delta sigma weight residual 1.529 1.518 0.011 1.04e-02 9.25e+03 1.14e+00 bond pdb=" CA GLU C 114 " pdb=" CB GLU C 114 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.58e-02 4.01e+03 7.67e-01 bond pdb=" CA GLU A 114 " pdb=" CB GLU A 114 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.58e-02 4.01e+03 7.63e-01 ... (remaining 3196 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 4024 0.99 - 1.98: 240 1.98 - 2.97: 35 2.97 - 3.96: 12 3.96 - 4.95: 12 Bond angle restraints: 4323 Sorted by residual: angle pdb=" CA GLU B 114 " pdb=" CB GLU B 114 " pdb=" CG GLU B 114 " ideal model delta sigma weight residual 114.10 118.34 -4.24 2.00e+00 2.50e-01 4.50e+00 angle pdb=" CA GLU A 114 " pdb=" CB GLU A 114 " pdb=" CG GLU A 114 " ideal model delta sigma weight residual 114.10 118.31 -4.21 2.00e+00 2.50e-01 4.44e+00 angle pdb=" CA GLU C 114 " pdb=" CB GLU C 114 " pdb=" CG GLU C 114 " ideal model delta sigma weight residual 114.10 118.28 -4.18 2.00e+00 2.50e-01 4.37e+00 angle pdb=" CB GLU C 114 " pdb=" CG GLU C 114 " pdb=" CD GLU C 114 " ideal model delta sigma weight residual 112.60 115.77 -3.17 1.70e+00 3.46e-01 3.48e+00 angle pdb=" CB GLU A 114 " pdb=" CG GLU A 114 " pdb=" CD GLU A 114 " ideal model delta sigma weight residual 112.60 115.76 -3.16 1.70e+00 3.46e-01 3.46e+00 ... (remaining 4318 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.87: 1536 11.87 - 23.74: 195 23.74 - 35.62: 117 35.62 - 47.49: 45 47.49 - 59.36: 15 Dihedral angle restraints: 1908 sinusoidal: 669 harmonic: 1239 Sorted by residual: dihedral pdb=" CA ALA B 208 " pdb=" C ALA B 208 " pdb=" N ASN B 209 " pdb=" CA ASN B 209 " ideal model delta harmonic sigma weight residual -180.00 -163.00 -17.00 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ALA A 208 " pdb=" C ALA A 208 " pdb=" N ASN A 209 " pdb=" CA ASN A 209 " ideal model delta harmonic sigma weight residual -180.00 -163.02 -16.98 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA ALA C 208 " pdb=" C ALA C 208 " pdb=" N ASN C 209 " pdb=" CA ASN C 209 " ideal model delta harmonic sigma weight residual -180.00 -163.03 -16.97 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 1905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 269 0.025 - 0.049: 158 0.049 - 0.073: 42 0.073 - 0.097: 20 0.097 - 0.122: 21 Chirality restraints: 510 Sorted by residual: chirality pdb=" CA ILE C 160 " pdb=" N ILE C 160 " pdb=" C ILE C 160 " pdb=" CB ILE C 160 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.70e-01 chirality pdb=" CA ILE B 160 " pdb=" N ILE B 160 " pdb=" C ILE B 160 " pdb=" CB ILE B 160 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.57e-01 chirality pdb=" CA ILE A 160 " pdb=" N ILE A 160 " pdb=" C ILE A 160 " pdb=" CB ILE A 160 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.51e-01 ... (remaining 507 not shown) Planarity restraints: 612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 222 " -0.004 2.00e-02 2.50e+03 7.93e-03 6.29e-01 pdb=" C GLY A 222 " 0.014 2.00e-02 2.50e+03 pdb=" O GLY A 222 " -0.005 2.00e-02 2.50e+03 pdb=" N ALA A 223 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 222 " -0.004 2.00e-02 2.50e+03 7.91e-03 6.26e-01 pdb=" C GLY B 222 " 0.014 2.00e-02 2.50e+03 pdb=" O GLY B 222 " -0.005 2.00e-02 2.50e+03 pdb=" N ALA B 223 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 222 " -0.004 2.00e-02 2.50e+03 7.83e-03 6.14e-01 pdb=" C GLY C 222 " 0.014 2.00e-02 2.50e+03 pdb=" O GLY C 222 " -0.005 2.00e-02 2.50e+03 pdb=" N ALA C 223 " -0.005 2.00e-02 2.50e+03 ... (remaining 609 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 1036 2.82 - 3.34: 2951 3.34 - 3.86: 5438 3.86 - 4.38: 6301 4.38 - 4.90: 12692 Nonbonded interactions: 28418 Sorted by model distance: nonbonded pdb=" OD1 ASN A 80 " pdb=" ND2 ASN A 145 " model vdw 2.295 3.120 nonbonded pdb=" OD1 ASN B 80 " pdb=" ND2 ASN B 145 " model vdw 2.295 3.120 nonbonded pdb=" OD1 ASN C 80 " pdb=" ND2 ASN C 145 " model vdw 2.296 3.120 nonbonded pdb=" O LYS B 116 " pdb=" ND2 ASN B 118 " model vdw 2.309 3.120 nonbonded pdb=" O LYS A 116 " pdb=" ND2 ASN A 118 " model vdw 2.309 3.120 ... (remaining 28413 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.850 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3201 Z= 0.162 Angle : 0.592 4.947 4323 Z= 0.314 Chirality : 0.039 0.122 510 Planarity : 0.002 0.008 612 Dihedral : 16.303 59.359 1104 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 0.00 % Allowed : 27.83 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.18 (0.40), residues: 414 helix: None (None), residues: 0 sheet: -0.91 (0.33), residues: 288 loop : -4.95 (0.20), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.001 0.000 TYR A 112 PHE 0.005 0.002 PHE A 183 HIS 0.001 0.000 HIS B 182 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 3201) covalent geometry : angle 0.59209 ( 4323) hydrogen bonds : bond 0.17210 ( 62) hydrogen bonds : angle 10.36933 ( 186) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.116 Fit side-chains REVERT: B 134 SER cc_start: 0.8811 (p) cc_final: 0.7879 (m) REVERT: C 112 TYR cc_start: 0.7251 (m-80) cc_final: 0.6077 (m-80) REVERT: C 150 GLN cc_start: 0.7053 (mm-40) cc_final: 0.6111 (mp10) REVERT: C 175 GLU cc_start: 0.7544 (tt0) cc_final: 0.6427 (mt-10) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.0497 time to fit residues: 6.5388 Evaluate side-chains 91 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 30.0000 chunk 26 optimal weight: 30.0000 chunk 2 optimal weight: 40.0000 chunk 16 optimal weight: 30.0000 chunk 32 optimal weight: 30.0000 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 22 optimal weight: 30.0000 chunk 37 optimal weight: 7.9990 overall best weight: 10.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A 136 ASN A 150 GLN A 185 ASN A 209 ASN B 76 ASN B 136 ASN B 185 ASN B 209 ASN C 76 ASN C 141 ASN C 209 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.128020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.106190 restraints weight = 4152.450| |-----------------------------------------------------------------------------| r_work (start): 0.4344 rms_B_bonded: 2.76 r_work: 0.4199 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 3201 Z= 0.346 Angle : 0.708 6.324 4323 Z= 0.381 Chirality : 0.043 0.124 510 Planarity : 0.003 0.012 612 Dihedral : 5.732 20.312 435 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 5.22 % Allowed : 24.93 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.42 (0.39), residues: 414 helix: None (None), residues: 0 sheet: -1.10 (0.32), residues: 291 loop : -5.10 (0.17), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR B 112 PHE 0.011 0.003 PHE C 183 HIS 0.003 0.002 HIS C 182 Details of bonding type rmsd covalent geometry : bond 0.00719 ( 3201) covalent geometry : angle 0.70760 ( 4323) hydrogen bonds : bond 0.02654 ( 62) hydrogen bonds : angle 6.29620 ( 186) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.125 Fit side-chains REVERT: B 76 ASN cc_start: 0.8859 (m-40) cc_final: 0.8391 (m110) REVERT: C 77 LEU cc_start: 0.9142 (tt) cc_final: 0.8908 (tt) REVERT: C 214 ASN cc_start: 0.8260 (m110) cc_final: 0.8052 (m110) outliers start: 18 outliers final: 17 residues processed: 95 average time/residue: 0.0498 time to fit residues: 6.0830 Evaluate side-chains 91 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 232 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 23 optimal weight: 0.7980 chunk 21 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 15 optimal weight: 30.0000 chunk 36 optimal weight: 30.0000 chunk 4 optimal weight: 9.9990 chunk 30 optimal weight: 30.0000 chunk 7 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 overall best weight: 10.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN A 153 GLN ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.125705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.104110 restraints weight = 4088.666| |-----------------------------------------------------------------------------| r_work (start): 0.4321 rms_B_bonded: 2.65 r_work: 0.4167 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3998 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 3201 Z= 0.321 Angle : 0.689 7.635 4323 Z= 0.361 Chirality : 0.041 0.124 510 Planarity : 0.003 0.011 612 Dihedral : 5.755 21.725 435 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 7.25 % Allowed : 22.90 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.67 (0.38), residues: 414 helix: None (None), residues: 0 sheet: -1.30 (0.31), residues: 291 loop : -5.12 (0.18), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.001 0.000 TYR C 112 PHE 0.010 0.003 PHE C 183 HIS 0.002 0.001 HIS C 182 Details of bonding type rmsd covalent geometry : bond 0.00659 ( 3201) covalent geometry : angle 0.68905 ( 4323) hydrogen bonds : bond 0.02212 ( 62) hydrogen bonds : angle 5.88375 ( 186) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.146 Fit side-chains REVERT: B 76 ASN cc_start: 0.8912 (m-40) cc_final: 0.8467 (m-40) REVERT: C 77 LEU cc_start: 0.9229 (tt) cc_final: 0.9010 (tt) REVERT: C 206 ASN cc_start: 0.8316 (OUTLIER) cc_final: 0.7645 (t0) outliers start: 25 outliers final: 20 residues processed: 95 average time/residue: 0.0476 time to fit residues: 5.9066 Evaluate side-chains 97 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 232 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 17 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 38 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 chunk 26 optimal weight: 20.0000 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.129976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.107243 restraints weight = 4013.277| |-----------------------------------------------------------------------------| r_work (start): 0.4355 rms_B_bonded: 2.78 r_work: 0.4202 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 3201 Z= 0.277 Angle : 0.648 7.801 4323 Z= 0.339 Chirality : 0.041 0.126 510 Planarity : 0.003 0.011 612 Dihedral : 5.642 21.928 435 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 8.99 % Allowed : 22.03 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.72 (0.37), residues: 414 helix: None (None), residues: 0 sheet: -1.33 (0.30), residues: 291 loop : -5.15 (0.18), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR A 112 PHE 0.008 0.003 PHE C 183 HIS 0.002 0.001 HIS B 182 Details of bonding type rmsd covalent geometry : bond 0.00568 ( 3201) covalent geometry : angle 0.64759 ( 4323) hydrogen bonds : bond 0.01920 ( 62) hydrogen bonds : angle 5.59712 ( 186) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 79 time to evaluate : 0.091 Fit side-chains REVERT: A 113 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7969 (tt0) REVERT: B 76 ASN cc_start: 0.8920 (m-40) cc_final: 0.8374 (m-40) REVERT: C 158 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8751 (mt) REVERT: C 206 ASN cc_start: 0.8155 (OUTLIER) cc_final: 0.7444 (t0) REVERT: C 214 ASN cc_start: 0.8245 (m110) cc_final: 0.7984 (m110) outliers start: 31 outliers final: 24 residues processed: 96 average time/residue: 0.0462 time to fit residues: 5.6998 Evaluate side-chains 105 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 210 ASN Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 232 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 18 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 41 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 chunk 44 optimal weight: 30.0000 chunk 6 optimal weight: 30.0000 chunk 17 optimal weight: 8.9990 chunk 5 optimal weight: 40.0000 chunk 21 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 overall best weight: 9.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN A 210 ASN ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.129203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.106860 restraints weight = 4071.740| |-----------------------------------------------------------------------------| r_work (start): 0.4342 rms_B_bonded: 2.77 r_work: 0.4189 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 3201 Z= 0.299 Angle : 0.655 7.444 4323 Z= 0.345 Chirality : 0.041 0.126 510 Planarity : 0.003 0.011 612 Dihedral : 5.763 22.185 435 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.32 % Favored : 87.68 % Rotamer: Outliers : 12.17 % Allowed : 19.13 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.87 (0.38), residues: 414 helix: None (None), residues: 0 sheet: -1.60 (0.30), residues: 303 loop : -5.02 (0.18), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR C 112 PHE 0.009 0.003 PHE B 55 HIS 0.001 0.001 HIS C 182 Details of bonding type rmsd covalent geometry : bond 0.00616 ( 3201) covalent geometry : angle 0.65489 ( 4323) hydrogen bonds : bond 0.01947 ( 62) hydrogen bonds : angle 5.57222 ( 186) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 74 time to evaluate : 0.105 Fit side-chains REVERT: B 76 ASN cc_start: 0.8907 (m-40) cc_final: 0.8395 (m-40) REVERT: C 206 ASN cc_start: 0.8152 (OUTLIER) cc_final: 0.7485 (t0) REVERT: C 214 ASN cc_start: 0.8282 (m110) cc_final: 0.8002 (m110) outliers start: 42 outliers final: 30 residues processed: 98 average time/residue: 0.0485 time to fit residues: 6.1083 Evaluate side-chains 106 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 75 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 210 ASN Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 232 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 15 optimal weight: 30.0000 chunk 8 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 16 optimal weight: 8.9990 chunk 36 optimal weight: 30.0000 chunk 33 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN A 210 ASN ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.130273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.106727 restraints weight = 4008.531| |-----------------------------------------------------------------------------| r_work (start): 0.4323 rms_B_bonded: 2.79 r_work: 0.4165 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 3201 Z= 0.278 Angle : 0.642 6.795 4323 Z= 0.338 Chirality : 0.040 0.126 510 Planarity : 0.003 0.011 612 Dihedral : 5.713 22.158 435 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.56 % Favored : 87.44 % Rotamer: Outliers : 10.14 % Allowed : 21.16 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.96 (0.37), residues: 414 helix: None (None), residues: 0 sheet: -1.66 (0.29), residues: 303 loop : -5.04 (0.18), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR C 112 PHE 0.008 0.003 PHE B 55 HIS 0.001 0.001 HIS C 182 Details of bonding type rmsd covalent geometry : bond 0.00577 ( 3201) covalent geometry : angle 0.64156 ( 4323) hydrogen bonds : bond 0.01861 ( 62) hydrogen bonds : angle 5.51091 ( 186) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 78 time to evaluate : 0.114 Fit side-chains REVERT: A 134 SER cc_start: 0.9074 (OUTLIER) cc_final: 0.8281 (m) REVERT: B 76 ASN cc_start: 0.8912 (m-40) cc_final: 0.8397 (m-40) REVERT: C 206 ASN cc_start: 0.8182 (OUTLIER) cc_final: 0.7505 (t0) REVERT: C 214 ASN cc_start: 0.8194 (m110) cc_final: 0.7888 (m110) outliers start: 35 outliers final: 30 residues processed: 97 average time/residue: 0.0468 time to fit residues: 5.9654 Evaluate side-chains 109 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 77 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 210 ASN Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 232 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 42 optimal weight: 20.0000 chunk 32 optimal weight: 30.0000 chunk 31 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 33 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 overall best weight: 9.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN A 210 ASN B 80 ASN ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.129561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.105878 restraints weight = 4084.035| |-----------------------------------------------------------------------------| r_work (start): 0.4321 rms_B_bonded: 2.82 r_work: 0.4171 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 3201 Z= 0.305 Angle : 0.658 7.290 4323 Z= 0.348 Chirality : 0.041 0.125 510 Planarity : 0.003 0.011 612 Dihedral : 5.834 22.582 435 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.29 % Favored : 86.71 % Rotamer: Outliers : 10.72 % Allowed : 21.45 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.05 (0.37), residues: 414 helix: None (None), residues: 0 sheet: -1.74 (0.29), residues: 303 loop : -5.05 (0.18), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR C 112 PHE 0.008 0.003 PHE B 55 HIS 0.001 0.001 HIS C 182 Details of bonding type rmsd covalent geometry : bond 0.00630 ( 3201) covalent geometry : angle 0.65827 ( 4323) hydrogen bonds : bond 0.01948 ( 62) hydrogen bonds : angle 5.53404 ( 186) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 72 time to evaluate : 0.123 Fit side-chains REVERT: A 114 GLU cc_start: 0.8067 (mp0) cc_final: 0.7689 (mp0) REVERT: A 134 SER cc_start: 0.9091 (OUTLIER) cc_final: 0.8296 (m) REVERT: A 150 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7465 (mm-40) REVERT: B 76 ASN cc_start: 0.8941 (m-40) cc_final: 0.8418 (m-40) REVERT: C 150 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.7062 (mm-40) REVERT: C 206 ASN cc_start: 0.8162 (OUTLIER) cc_final: 0.7473 (t0) REVERT: C 214 ASN cc_start: 0.8211 (m110) cc_final: 0.7895 (m110) outliers start: 37 outliers final: 29 residues processed: 93 average time/residue: 0.0460 time to fit residues: 5.5893 Evaluate side-chains 104 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 71 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 232 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 9.9990 chunk 11 optimal weight: 30.0000 chunk 41 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 12 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 35 optimal weight: 30.0000 chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.129866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.106725 restraints weight = 4077.934| |-----------------------------------------------------------------------------| r_work (start): 0.4338 rms_B_bonded: 2.78 r_work: 0.4188 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 3201 Z= 0.284 Angle : 0.650 7.005 4323 Z= 0.342 Chirality : 0.040 0.125 510 Planarity : 0.003 0.011 612 Dihedral : 5.787 22.520 435 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.56 % Favored : 87.44 % Rotamer: Outliers : 9.86 % Allowed : 22.61 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.08 (0.37), residues: 414 helix: None (None), residues: 0 sheet: -1.76 (0.29), residues: 303 loop : -5.05 (0.18), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR C 112 PHE 0.008 0.003 PHE B 55 HIS 0.001 0.001 HIS C 182 Details of bonding type rmsd covalent geometry : bond 0.00588 ( 3201) covalent geometry : angle 0.64960 ( 4323) hydrogen bonds : bond 0.01866 ( 62) hydrogen bonds : angle 5.49249 ( 186) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 0.120 Fit side-chains REVERT: A 114 GLU cc_start: 0.8061 (mp0) cc_final: 0.7664 (mp0) REVERT: A 134 SER cc_start: 0.9094 (OUTLIER) cc_final: 0.8327 (m) REVERT: B 76 ASN cc_start: 0.8928 (m-40) cc_final: 0.8412 (m-40) REVERT: C 77 LEU cc_start: 0.9175 (tt) cc_final: 0.8929 (tt) REVERT: C 206 ASN cc_start: 0.8145 (OUTLIER) cc_final: 0.7462 (t0) REVERT: C 214 ASN cc_start: 0.8201 (m110) cc_final: 0.7876 (m110) REVERT: C 233 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8956 (mp) outliers start: 34 outliers final: 31 residues processed: 98 average time/residue: 0.0405 time to fit residues: 5.2746 Evaluate side-chains 113 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 210 ASN Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 233 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 6 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 chunk 15 optimal weight: 30.0000 chunk 33 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 8 optimal weight: 5.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN A 210 ASN B 80 ASN ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.130219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.107510 restraints weight = 4046.173| |-----------------------------------------------------------------------------| r_work (start): 0.4333 rms_B_bonded: 2.75 r_work: 0.4172 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 3201 Z= 0.273 Angle : 0.646 7.475 4323 Z= 0.340 Chirality : 0.040 0.125 510 Planarity : 0.002 0.011 612 Dihedral : 5.739 22.378 435 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.53 % Favored : 86.47 % Rotamer: Outliers : 11.01 % Allowed : 21.74 % Favored : 67.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.12 (0.37), residues: 414 helix: None (None), residues: 0 sheet: -1.79 (0.29), residues: 303 loop : -5.06 (0.18), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR C 112 PHE 0.008 0.003 PHE B 55 HIS 0.001 0.001 HIS C 182 Details of bonding type rmsd covalent geometry : bond 0.00566 ( 3201) covalent geometry : angle 0.64597 ( 4323) hydrogen bonds : bond 0.01875 ( 62) hydrogen bonds : angle 5.45264 ( 186) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 79 time to evaluate : 0.161 Fit side-chains REVERT: A 114 GLU cc_start: 0.8076 (mp0) cc_final: 0.7670 (mp0) REVERT: A 134 SER cc_start: 0.9081 (OUTLIER) cc_final: 0.8307 (m) REVERT: B 76 ASN cc_start: 0.8909 (m-40) cc_final: 0.8413 (m-40) REVERT: C 77 LEU cc_start: 0.9186 (tt) cc_final: 0.8940 (tt) REVERT: C 206 ASN cc_start: 0.8141 (OUTLIER) cc_final: 0.7486 (t0) REVERT: C 214 ASN cc_start: 0.8202 (m110) cc_final: 0.7883 (m110) outliers start: 38 outliers final: 33 residues processed: 100 average time/residue: 0.0492 time to fit residues: 6.3754 Evaluate side-chains 111 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 76 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 210 ASN Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 232 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 40 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 35 optimal weight: 20.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN A 210 ASN ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.131064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.108275 restraints weight = 3987.646| |-----------------------------------------------------------------------------| r_work (start): 0.4350 rms_B_bonded: 2.74 r_work: 0.4200 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3201 Z= 0.262 Angle : 0.649 7.497 4323 Z= 0.339 Chirality : 0.040 0.125 510 Planarity : 0.002 0.011 612 Dihedral : 5.722 22.243 435 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.29 % Favored : 86.71 % Rotamer: Outliers : 9.86 % Allowed : 22.32 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.11 (0.37), residues: 414 helix: None (None), residues: 0 sheet: -1.78 (0.29), residues: 303 loop : -5.07 (0.17), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR C 112 PHE 0.008 0.002 PHE B 55 HIS 0.001 0.001 HIS C 182 Details of bonding type rmsd covalent geometry : bond 0.00545 ( 3201) covalent geometry : angle 0.64869 ( 4323) hydrogen bonds : bond 0.01844 ( 62) hydrogen bonds : angle 5.41701 ( 186) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 74 time to evaluate : 0.095 Fit side-chains REVERT: A 114 GLU cc_start: 0.8056 (mp0) cc_final: 0.7639 (mp0) REVERT: A 134 SER cc_start: 0.9056 (OUTLIER) cc_final: 0.8276 (m) REVERT: B 76 ASN cc_start: 0.8928 (m-40) cc_final: 0.8443 (m-40) REVERT: C 206 ASN cc_start: 0.8139 (OUTLIER) cc_final: 0.7476 (t0) REVERT: C 214 ASN cc_start: 0.8187 (m110) cc_final: 0.7857 (m110) outliers start: 34 outliers final: 32 residues processed: 94 average time/residue: 0.0435 time to fit residues: 5.2646 Evaluate side-chains 108 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 74 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 210 ASN Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 232 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 29 optimal weight: 5.9990 chunk 27 optimal weight: 30.0000 chunk 16 optimal weight: 20.0000 chunk 2 optimal weight: 30.0000 chunk 28 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 35 optimal weight: 30.0000 chunk 7 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.131867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.108988 restraints weight = 4047.094| |-----------------------------------------------------------------------------| r_work (start): 0.4364 rms_B_bonded: 2.76 r_work: 0.4214 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3201 Z= 0.235 Angle : 0.630 7.304 4323 Z= 0.328 Chirality : 0.040 0.125 510 Planarity : 0.002 0.010 612 Dihedral : 5.607 22.089 435 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.04 % Favored : 86.96 % Rotamer: Outliers : 8.70 % Allowed : 24.06 % Favored : 67.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.09 (0.37), residues: 414 helix: None (None), residues: 0 sheet: -1.76 (0.29), residues: 303 loop : -5.07 (0.17), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR C 112 PHE 0.007 0.002 PHE B 55 HIS 0.001 0.001 HIS C 182 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 3201) covalent geometry : angle 0.62999 ( 4323) hydrogen bonds : bond 0.01780 ( 62) hydrogen bonds : angle 5.35288 ( 186) =============================================================================== Job complete usr+sys time: 750.04 seconds wall clock time: 13 minutes 40.87 seconds (820.87 seconds total)